Spectroscopic analysis and conventional and phase-sensitive flow cytometry were used to compare changes in PI and EB fluorescence intensity and lifetime bound to DNA and fixed Chinese hamster ovary (CHO) cells in the presence of D2O versus phosphate buffered saline (PBS). A two-fold enhancement of fluorescence intensity of PI and EB bound to fixed-CHO cells in D2O was noted as well as a 5 ns increase in PI and EB fluorescence lifetimes in D2O. Apoptotic sub-populations of HL-60 cells had a significantly reduced fluorescence lifetime compared to non-apoptotic sub-populations. Results indicate that different chromatin states, or differences in the structures of PI and EB lead to alterations in the fluorescence intensity and fluorescence lifetime of these intercalating probes.